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mcmc.c
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mcmc.c
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/*
* MrBayes 3
*
* (c) 2002-2023
*
* John P. Huelsenbeck
* Dept. Integrative Biology
* University of California, Berkeley
* Berkeley, CA 94720-3140
* johnh@berkeley.edu
*
* Fredrik Ronquist
* Swedish Museum of Natural History
* Box 50007
* SE-10405 Stockholm, SWEDEN
* fredrik.ronquist@nrm.se
*
* With important contributions by
*
* Paul van der Mark (paulvdm@sc.fsu.edu)
* Maxim Teslenko (maxkth@gmail.com)
* Chi Zhang (zhangchicool@gmail.com)
*
* and by many users (run 'acknowledgments' to see more info)
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details (www.gnu.org).
*
*/
#undef DEBUG_TIME
#if defined (DEBUG_TIME)
#define _POSIX_C_SOURCE 199309L
#include <sys/time.h>
#endif
#include "bayes.h"
#include "best.h"
#include "command.h"
#include "likelihood.h"
#include "mbbeagle.h"
#include "mcmc.h"
#include "model.h"
#include "proposal.h"
#include "sumpt.h"
#include "utils.h"
#if defined(__MWERKS__)
#include "SIOUX.h"
#endif
#include <signal.h>
#include <limits.h>
#if defined (WIN_VERSION) && !defined (__GNUC__)
#define VISUAL
#else
typedef void (*sighandler_t) (int);
#endif
#define GIBBS_SAMPLE_FREQ 100 /* generations between gibbs sampling of gamma cats */
#define MAX_SMALL_JUMP 10 /* threshold for precalculating trans probs of adgamma model */
#define BIG_JUMP 100 /* threshold for using stationary approximation */
#define MAX_RUNS 120 /* maximum number of independent runs */
#define PFILE 0
#define TFILE 1
#define CALFILE 2
#define MCMCFILE 3
#define MAXTUNINGPARAM 10000 /* limit to ensure convergence for autotuning */
#define SAMPLE_ALL_SS /* if defined makes ss sample every generation instead of every sample frequency */
#define BEAGLE_RESCALE_FREQ 160
#define BEAGLE_RESCALE_FREQ_DOUBLE 10 /* The factor by which BEAGLE_RESCALE_FREQ get multiplied if double precision is used */
#define TARGETLENDELTA 100
/* debugging compiler statements */
#undef DEBUG_SETUPTERMSTATE
#undef DEBUG_RUNCHAIN
#undef DEBUG_NOSHORTCUTS
#undef DEBUG_NOSCALING
#undef DEBUG_TIPROBS_STD
#undef DEBUG_RUN_WITHOUT_DATA
#undef DEBUG_CONSTRAINTS
#undef DEBUG_LNLIKELIHOOD /* slow if defined!! */
#undef DEBUG_LIKELIHOOD
#undef DEBUG_FBDPR // #undef FBDPR_CondOnN
#undef SHOW_MOVE
#if defined (MPI_ENABLED)
#define ERROR_TEST2(failString,X1,X2) \
MPI_Allreduce (&nErrors, &sumErrors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);\
if (sumErrors > 0)\
{\
MrBayesPrint ("%s "failString"\n", spacer);\
X1;X2;\
}
#else
#define ERROR_TEST2(failString,X1,X2) \
if (nErrors > 0)\
{\
MrBayesPrint ("%s "failString"\n", spacer);\
X1;X2;\
}
#endif
/* local (to this file) data types */
typedef struct pfnode
{
struct pfnode *left;
struct pfnode *right;
int *count;
BitsLong *partition;
} PFNODE;
/* local prototypes */
int AddTreeSamples (int from, int to, int saveToList);
PFNODE *AddPartition (PFNODE *r, BitsLong *p, int runId);
int AddTreeToPartitionCounters (Tree *tree, int treeId, int runId);
int AttemptSwap (int swapA, int swapB, RandLong *seed);
void BuildExhaustiveSearchTree (Tree *t, int chain, int nTaxInTree, TreeInfo *tInfo);
int BuildStepwiseTree (Tree *t, int chain, RandLong *seed);
int CalcLikeAdgamma (int d, Param *param, int chain, MrBFlt *lnL);
void CalcPartFreqStats (PFNODE *p, STATS *stat);
void CalcTopoConvDiagn (int numSamples);
#ifdef VISUAL
BOOL WINAPI CatchInterrupt (DWORD signum);
#else
void CatchInterrupt (int signum);
#endif
int CheckTemperature (void);
void CloseMBPrintFiles (void);
PFNODE *CompactTree (PFNODE *p);
int ConfirmAbortRun(void);
void CopyParams (int chain);
void CopyPFNodeDown (PFNODE *p);
void CopyTrees (int chain);
int ExtendChainQuery (void);
int FillNumSitesOfPat (void);
TreeNode *FindBestNode (Tree *t, TreeNode *p, TreeNode *addNode, CLFlt *minLength, int chain);
void FreeChainMemory (void);
MrBFlt GetFitchPartials (ModelInfo *m, int chain, int source1, int source2, int destination);
void GetStamp (void);
void GetSwappers (int *swapA, int *swapB, int run);
void GetTempDownPassSeq (TreeNode *p, int *i, TreeNode **dp);
int GetTotalRateShifts (Model *mp, MrBFlt *shiftTimes);
MrBFlt GibbsSampleGamma (int chain, int division, RandLong *seed);
int InitAdGamma(void);
int InitChainCondLikes (void);
int InitClockBrlens (Tree *t);
int InitEigenSystemInfo (ModelInfo *m);
int InitInvCondLikes (void);
int InitParsSets (void);
int InitPrintParams (void);
int IsPFNodeEmpty (PFNODE *p);
PFNODE *LargestNonemptyPFNode (PFNODE *p, int *i, int j);
MrBFlt LogLike (int chain);
MrBFlt LogPrior (int chain);
int LnBirthDeathPriorPrRandom (Tree *t, MrBFlt clockRate, MrBFlt *prob, MrBFlt sR, MrBFlt eR, MrBFlt sF);
int LnBirthDeathPriorPrDiversity (Tree *t, MrBFlt clockRate, MrBFlt *prob, MrBFlt sR, MrBFlt eR, MrBFlt sF);
int LnBirthDeathPriorPrCluster (Tree *t, MrBFlt clockRate, MrBFlt *prob, MrBFlt sR, MrBFlt eR, MrBFlt sF);
int LnFossilizedBDPriorFossilTip (Tree *t, MrBFlt clockRate, MrBFlt *prob, MrBFlt *sR, MrBFlt *eR, MrBFlt *fR, MrBFlt sF);
int LnFossilizedBDPriorRandom (Tree *t, MrBFlt clockRate, MrBFlt *prob, MrBFlt *lambda, MrBFlt *mu, MrBFlt *psi, MrBFlt *rho, MrBFlt *t_sl, int n_sl);
int LnFossilizedBDPriorDiversity (Tree *t, MrBFlt clockRate, MrBFlt *prob, MrBFlt *lambda, MrBFlt *mu, MrBFlt *psi, MrBFlt *rho, MrBFlt *t_sl, int n_sl);
MrBFlt LnP0 (MrBFlt t, MrBFlt l, MrBFlt m);
MrBFlt LnP0Subsample (MrBFlt t, MrBFlt l, MrBFlt m, MrBFlt f);
MrBFlt LnP1 (MrBFlt t, MrBFlt l, MrBFlt m);
MrBFlt LnP1Subsample (MrBFlt t, MrBFlt l, MrBFlt m, MrBFlt f);
MrBFlt LnP0_fossil (MrBFlt t, MrBFlt lambda, MrBFlt mu, MrBFlt psi, MrBFlt c1, MrBFlt c2);
MrBFlt LnP1_fossil (MrBFlt t, MrBFlt rho, MrBFlt c1, MrBFlt c2);
MrBFlt LnQi_fossil (MrBFlt t, MrBFlt *t_f, int sl, MrBFlt *c1, MrBFlt *c2);
MrBFlt LnPi_fossil (MrBFlt t, MrBFlt *t_f, int sl, MrBFlt *c1, MrBFlt *c2, MrBFlt *lambda, MrBFlt *mu, MrBFlt *psi);
int NewtonRaphsonBrlen (Tree *t, TreeNode *p, int chain);
void NodeToNodeDistances (Tree *t, TreeNode *fromNode);
int PickProposal (RandLong *seed, int chainIndex);
int NumCppEvents (Param *p, int chain);
int PosSelProbs (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int PosSelProbs_SSE (TreeNode *p, int division, int chain);
#endif
int PreparePrintFiles (void);
int PrintAncStates_Bin (TreeNode *p, int division, int chain);
int PrintAncStates_Gen (TreeNode *p, int division, int chain);
int PrintAncStates_NUC4 (TreeNode *p, int division, int chain);
int PrintAncStates_Std (TreeNode *p, int division, int chain);
int PrintCheckPoint (long long gen);
int PrintMCMCDiagnosticsToFile (long long curGen);
#if defined (MPI_ENABLED)
int PrintMPISlaves (FILE *fp);
#endif
void PrintParamValues (Param *p, int chain, char *s);
int PrintParsMatrix (void);
int PrintSiteRates_Gen (TreeNode *p, int division, int chain);
int PrintSiteRates_Std (TreeNode *p, int division, int chain);
int PrintStates (long long curGen, int coldId);
int PrintStatesToFiles (long long curGen);
int PrintSwapInfo (void);
int PrintTermState (void);
void PrintTiProbs (CLFlt *tP, MrBFlt *bs, int nStates);
int PrintTopConvInfo (void);
void PrintToScreen (long long curGen, long long startGen, time_t endingT, time_t startingT);
int PrintTree (long long curGen, Param *treeParam, int chain, int showBrlens, MrBFlt clockRate);
MrBFlt PropAncFossil (Param *param, int chain);
#if defined (MPI_ENABLED)
int ReassembleMoveInfo (void);
int ReassembleParamVals (int *curId);
int ReassembleSwapInfo (void);
int ReassembleTuningParams (void);
void RedistributeMoveInfo (void);
int RedistributeParamVals (void);
int RedistributeTuningParams (void);
#endif
int RemovePartition (PFNODE *r, BitsLong *p, int runId);
int RemoveTreeFromPartitionCounters (Tree *tree, int treeId, int runId);
int RemoveTreeSamples (int from, int to);
int ReopenMBPrintFiles (void);
void ResetChainIds (void);
void ResetFlips(int chain);
int ReusePreviousResults(int *numSamples, int);
int RunChain (RandLong *seed);
int SafeSprintf (char **target, int *targetLen, char *fmt, ...);
void SetChainIds (void);
void SetFileNames (void);
int SetLikeFunctions (void);
int SetLocalChainsAndDataSplits (void);
int SetModelInfo (void);
int SetMoves (void);
int SetBinaryQMatrix (MrBFlt **a, int whichChain, int division);
int SetNucQMatrix (MrBFlt **a, int n, int whichChain, int division, MrBFlt rateMult, MrBFlt *rA, MrBFlt *rS);
int SetProteinQMatrix (MrBFlt **a, int n, int whichChain, int division, MrBFlt rateMult);
int SetStdQMatrix (MrBFlt **a, int nStates, MrBFlt *bs, int cType);
int SetUpPartitionCounters (void);
int SetUpTermState (void);
int SetUsedMoves (void);
int ShowMoveSummary (void);
void ShowValuesForChain (int chn);
int SiteOmegas (TreeNode *p, int division, int chain);
#if defined (SSE_ENABLED)
int SiteOmegas_SSE (TreeNode *p, int division, int chain);
#endif
PFNODE *SmallestNonemptyPFNode (PFNODE *p, int *i, int j);
PFNODE *Talloc (void);
void Tfree (PFNODE *r);
MrBFlt Temperature (int x);
void TouchAllCijks (int chain);
void TouchAllPartitions (void);
void TouchAllTrees (int chain);
void TouchEverything (int chain);
/* globals declared here and used elsewhere */
int *bsIndex; /* compressed std stat freq index */
Chain chainParams; /* parameters of Markov chain */
int *compCharPos; /* char position in compressed matrix */
int *compColPos; /* column position in compressed matrix */
BitsLong *compMatrix; /* compressed character matrix */
int compMatrixRowSize; /* row size of compressed matrix */
char inputFileName[100]; /* input (NEXUS) file name */
MoveType moveTypes[NUM_MOVE_TYPES]; /* holds information on the move types */
int numCompressedChars; /* number of compressed characters */
int numMoveTypes; /* the number of move types */
CLFlt *numSitesOfPat; /* no. sites of each pattern */
int *origChar; /* index from compressed char to original char */
char stamp[11]; /* holds a unique identifier for each analysis */
MrBFlt *stdStateFreqs; /* std char state frequencies */
int *stdType; /* compressed std char type: ord, unord, irrev */
int *tiIndex; /* compressed std char ti index */
#if defined (BEAGLE_ENABLED)
int recalcScalers; /* should we recalculate scalers for current state YES/NO */
#endif
/* globals used here but declared elsewhere (in likelihood.c) */
extern CLFlt *preLikeL; /* precalculated cond likes for left descendant */
extern CLFlt *preLikeR; /* precalculated cond likes for right descendant*/
extern CLFlt *preLikeA; /* precalculated cond likes for ancestor */
/* local (to this file) variables */
int numLocalChains; /* number of Markov chains */
int *chainId = NULL; /* information on the id (0 ...) of the chain */
MrBFlt *curLnL = NULL; /* stores log likelihood */
MrBFlt *curLnPr = NULL; /* stores log prior probability */
int stepRelativeBurninSS; /* Should we use relative burn in within each step or not */
MrBFlt powerSS; /* power (beta) in power posterior distribution used in SS */
MrBFlt *marginalLnLSS = NULL; /* marginal likelihood obtained using steppingstone sampling */
MrBFlt *stepAcumulatorSS = NULL; /* accumulates likelihoods for current step in SS */
MrBFlt *stepScalerSS = NULL; /* scaler of stepAcumulatorSS in log scale in SS */
MrBFlt *splitfreqSS = NULL; /* array holding split frequencies for each step in SS */
int *sympiIndex; /* sympi state freq index for multistate chars */
int stdStateFreqsRowSize; /* row size for std state frequencies */
int *weight; /* weight of each compressed char */
int *chainTempId; /* info ton temp, change to float holding temp? */
int state[MAX_CHAINS]; /* state of chain */
int augmentData; /* are data being augmented for any division? */
int *nAccepted; /* counter of accepted moves */
int *termState = NULL; /* stores character states of tips */
int *isPartAmbig = NULL; /* records whether tips are partially ambiguous */
BitsLong **parsPtrSpace = NULL; /* space holding pointers to parsimony sets */
BitsLong ***parsPtr = NULL; /* pointers to pars state sets for chain & node */
CLFlt *parsNodeLengthSpace = NULL; /* space for parsimony node lengths */
CLFlt **parsNodeLen = NULL; /* pointers to pars node lengths for chains */
char *printString; /* string for printing to a file */
size_t printStringSize; /* length of printString */
MCMCMove **usedMoves; /* vector of pointers to used moves */
int numUsedMoves; /* the number of moves used by chain */
Param **printParam; /* vector of pointers to normal params to print */
int numPrintParams; /* the number of normal params to print */
Param **printTreeParam; /* vector of pointers to tree params to print */
Param **topologyParam; /* vector of pointers to topology params */
int numPrintTreeParams; /* the number of tree params to print */
int codon[6][64]; /* holds info on amino acids coded in code */
int chainHasAdgamma; /* indicates if chain has adgamma HMMs */
int inferPosSel; /* indicates if positive selection is inferred */
MrBFlt *posSelProbs; /* probs. for positive selection */
int hasMarkovTi[MAX_SMALL_JUMP]; /* vector marking size of observed HMM jumps */
int *siteJump; /* vector of sitejumps for adgamma model */
MrBFlt **rateProbs; /* pointers to rate probs used by adgamma model */
MrBFlt *rateProbSpace; /* space for rate probs used by adgamma model */
int rateProbRowSize; /* size of rate probs for one chain one state */
MrBFlt **markovTi[MAX_SMALL_JUMP]; /* trans prob matrices used in calc of adgamma */
MrBFlt **markovTiN; /* trans prob matrices used in calc of adgamma */
int whichReweightNum; /* used for setting reweighting of char pats */
int ***swapInfo; /* keeps track of attempts & successes of swaps */
int tempIndex; /* keeps track of which user temp is specified */
int abortMove; /* flag determining whether to abort move */
PFNODE **partFreqTreeRoot; /* root of tree(s) holding partition freqs */
int nLongsNeeded; /* number of longs needed for partitions */
BitsLong **partition; /* matrix holding partitions */
MrBFlt *maxLnL0 = NULL; /* maximum likelihood */
FILE *fpMcmc = NULL; /* pointer to .mcmc file */
FILE **fpParm = NULL; /* pointer to .p file(s) */
FILE ***fpTree = NULL; /* pointer to .t file(s) */
FILE *fpSS = NULL; /* pointer to .ss file */
static int requestAbortRun; /* flag for aborting mcmc analysis */
int *topologyPrintIndex; /* print file index of each topology */
int *printTreeTopologyIndex; /* topology index of each tree print file */
long long numPreviousGen; /* number of generations in run to append to */
#if defined (MPI_ENABLED)
int lowestLocalRunId; /* lowest local run Id */
int highestLocalRunId; /* highest local run Id */
#endif
#if defined (PRINT_DUMP)
FILE **fpDump = NULL; /* pointer to .dump file(s) */
#endif
/* AddPartition: Add a partition to the tree keeping track of partition frequencies */
PFNODE *AddPartition (PFNODE *r, BitsLong *p, int runId)
{
int i, comp;
if (r == NULL)
{
/* new partition */
r = Talloc (); /* create a new node */
if (r == NULL)
return NULL;
for (i=0; i<nLongsNeeded; i++)
r->partition[i] = p[i];
for (i=0; i<chainParams.numRuns; i++)
r->count[i] = 0;
r->count[runId] = 1;
r->left = r->right = NULL;
}
else
{
for (i=0; i<nLongsNeeded; i++)
{
if (r->partition[i] != p[i])
break;
}
if (i == nLongsNeeded)
comp = 0;
else if (r->partition[i] < p[i])
comp = -1;
else
comp = 1;
if (comp == 0) /* repeated partition */
r->count[runId]++;
else if (comp < 0) /* greater than -> into left subtree */
{
if ((r->left = AddPartition (r->left, p, runId)) == NULL)
{
Tfree (r);
return NULL;
}
}
else
{
/* smaller than -> into right subtree */
if ((r->right = AddPartition (r->right, p, runId)) == NULL)
{
Tfree (r);
return NULL;
}
}
}
return r;
}
int AddToPrintString (char *tempStr)
{
size_t len1, len2;
len1 = strlen(printString);
len2 = strlen(tempStr);
if (len1 + len2 + 5 > printStringSize)
{
printStringSize += len1 + len2 - printStringSize + 200;
printString = (char*)SafeRealloc((void*)printString, printStringSize * sizeof(char));
if (!printString)
{
MrBayesPrint ("%s Problem reallocating printString (%d)\n", spacer, printStringSize * sizeof(char));
goto errorExit;
}
}
strcat(printString, tempStr);
// printf ("printString(%d) -> \"%s\"\n", printStringSize, printString);
return (NO_ERROR);
errorExit:
return (ERROR);
}
/* AddTreeSamples: Add tree samples from .t files to partition counters. if saveToList == YES then also save trees in tree list */
int AddTreeSamples (int from, int to, int saveToList)
{
int i, j, k, longestLine;
BitsLong lastBlock;
char *word, *s, *lineBuf;
FILE *fp;
Tree *t;
char *tempStr;
int tempStrSize = TEMPSTRSIZE;
if (from > to)
return (NO_ERROR);
# if defined (MPI_ENABLED)
if (proc_id != 0)
return (NO_ERROR);
# endif
tempStr = (char *) SafeMalloc((size_t)tempStrSize * sizeof(char));
if (!tempStr)
{
MrBayesPrint ("%s Problem allocating tempString (%d)\n", spacer, tempStrSize * sizeof(char));
return (ERROR);
}
for (i=0; i<numTopologies; i++)
{
t = chainParams.dtree;
for (j=0; j<chainParams.numRuns; j++)
{
if (numPrintTreeParams == 1)
{
if (chainParams.numRuns == 1)
SafeSprintf (&tempStr, &tempStrSize, "%s.t", chainParams.chainFileName);
else
SafeSprintf (&tempStr, &tempStrSize, "%s.run%d.t", chainParams.chainFileName, j+1);
}
else
{
if (chainParams.numRuns == 1)
SafeSprintf (&tempStr, &tempStrSize, "%s.tree%d.t", chainParams.chainFileName, i+1);
else
SafeSprintf (&tempStr, &tempStrSize, "%s.tree%d.run%d.t", chainParams.chainFileName, i+1, j+1);
}
if ((fp = OpenBinaryFileR (tempStr)) == NULL)
{
MrBayesPrint ("%s Problem opening file %s.\n", spacer, tempStr);
free (tempStr);
return (ERROR);
}
longestLine = LongestLine (fp);
SafeFclose (&fp);
if ((fp = OpenTextFileR (tempStr)) == NULL)
{
free (tempStr);
return (ERROR);
}
lineBuf = (char *) SafeCalloc (longestLine + 10, sizeof (char));
if (!lineBuf)
{
SafeFclose (&fp);
free (tempStr);
return (ERROR);
}
lastBlock = LastBlock (fp, lineBuf, longestLine);
fseek (fp, lastBlock, SEEK_SET);
for (k=1; k<=to; k++)
{
do {
if (fgets (lineBuf, longestLine, fp) == NULL)
{
SafeFclose (&fp);
free (lineBuf);
free (tempStr);
return ERROR;
}
word = strtok (lineBuf, " ");
} while (strcmp (word, "tree") != 0);
if (k>=from)
{
s = strtok (NULL, ";");
while (*s != '(')
s++;
StripComments(s);
if (ResetTopology (t, s) == ERROR)
{
SafeFclose (&fp);
free (lineBuf);
free (tempStr);
return ERROR;
}
if (AddTreeToPartitionCounters (t, i, j) == ERROR)
{
SafeFclose (&fp);
free (lineBuf);
free (tempStr);
return ERROR;
}
if (saveToList == YES)
if (AddToTreeList(&chainParams.treeList[numTopologies*j+i],t) == ERROR)
return (ERROR);
}
}
SafeFclose (&fp);
free (lineBuf);
} /* next run */
} /* next tree */
free (tempStr);
return (NO_ERROR);
}
/* AddTreeToPartitionCounters: Break a tree into partitions and add those to counters */
int AddTreeToPartitionCounters (Tree *tree, int treeId, int runId)
{
int i, j, nTaxa;
TreeNode *p;
if (tree->isRooted == YES)
nTaxa = tree->nNodes - tree->nIntNodes - 1;
else
nTaxa = tree->nNodes - tree->nIntNodes;
for (i=0; i<nTaxa; i++)
{
ClearBits(partition[i], nLongsNeeded);
SetBit(i, partition[i]);
}
for (i=0; i<tree->nIntNodes-1; i++)
{
p = tree->intDownPass[i];
assert (p->index >= tree->nNodes - tree->nIntNodes - (tree->isRooted == YES ? 1 : 0));
for (j=0; j<nLongsNeeded; j++)
{
partition[p->index][j] = partition[p->left->index][j] | partition[p->right->index][j];
}
if ((partFreqTreeRoot[treeId] = AddPartition (partFreqTreeRoot[treeId], partition[p->index], runId)) == NULL)
{
MrBayesPrint ("%s Could not allocate space for new partition in AddTreeToPartitionCounters\n", spacer);
return ERROR;
}
}
return NO_ERROR;
}
int AttemptSwap (int swapA, int swapB, RandLong *seed)
{
int d, tempX, reweightingChars, isSwapSuccessful, chI, chJ, runId;
MrBFlt tempA, tempB, lnLikeA, lnLikeB, lnPriorA, lnPriorB, lnR, r,
lnLikeStateAonDataB=0.0, lnLikeStateBonDataA=0.0, lnL;
ModelInfo *m;
Tree *tree;
# if defined (MPI_ENABLED)
int numChainsForProc, tempIdA=0, tempIdB=0, proc, procIdForA=0, procIdForB=0, tempIdMy=0, procIdPartner=0,
whichElementA=0, whichElementB=0, lower, upper, areWeA, doISwap, ierror,
myId, partnerId, i, run;
MrBFlt swapRan;
MPI_Status status[2];
MPI_Request request[2];
# endif
# if defined (MPI_ENABLED)
/* get the number of chains handled by this proc */
/* the number will be corrected further down for unbalanced scenarios */
numChainsForProc = (int) (chainParams.numChains * chainParams.numRuns / num_procs);
# endif
/* are we using character reweighting? */
reweightingChars = NO;
if ((chainParams.weightScheme[0] + chainParams.weightScheme[1]) > 0.00001)
reweightingChars = YES;
# if defined (MPI_ENABLED)
/* figure out processors involved in swap */
lower = upper = 0;
for (proc=0; proc<num_procs; proc++)
{
/* assign or increment chain id */
if (proc < (chainParams.numChains * chainParams.numRuns) % num_procs)
upper += numChainsForProc+1;
else
upper += numChainsForProc;
/* if swapA lies between lower and upper
* chain id's we know that this is the proc
* swapA is in */
if (swapA >= lower && swapA < upper)
{
procIdForA = proc;
whichElementA = swapA - lower;
}
if (swapB >= lower && swapB < upper)
{
procIdForB = proc;
whichElementB = swapB - lower;
}
lower = upper;
}
/* NOTE: at this point, procIdForA and procIdForB *
* store the proc id's of swapping procs. Also, *
* whichElementA and whichElementB store the *
* chainId[] index of swapping procs */
/* figure out if I am involved in the swap */
doISwap = areWeA = NO;
if (proc_id == procIdForA)
{
doISwap = YES;
areWeA = YES;
}
else if (proc_id == procIdForB)
{
doISwap = YES;
}
/* chain's that do not swap, continue to the next iteration */
if (doISwap == YES)
{
/* no need to communicate across processors if swapping chains are in the same proc */
if (procIdForA == procIdForB)
{
if (reweightingChars == YES)
{
/* use character reweighting */
lnLikeStateAonDataB = 0.0;
for (d=0; d<numCurrentDivisions; d++)
{
m = &modelSettings[d];
tree = GetTree(m->brlens, whichElementA, state[whichElementA]);
lnL = 0.0;
m->Likelihood (tree->root->left, d, whichElementA, &lnL, chainId[whichElementB] % chainParams.numChains);
lnLikeStateAonDataB += lnL;
}
lnLikeStateBonDataA = 0.0;
for (d=0; d<numCurrentDivisions; d++)
{
m = &modelSettings[d];
tree = GetTree(m->brlens, whichElementB, state[whichElementB]);
lnL = 0.0;
m->Likelihood (tree->root->left, d, whichElementB, &lnL, chainId[whichElementA] % chainParams.numChains);
lnLikeStateBonDataA += lnL;
}
}
/*curLnPr[whichElementA] = LogPrior(whichElementA);
curLnPr[whichElementB] = LogPrior(whichElementB);*/
/* then do the serial thing - simply swap chain id's */
tempA = Temperature (chainId[whichElementA]);
tempB = Temperature (chainId[whichElementB]);
lnLikeA = curLnL[whichElementA];
lnLikeB = curLnL[whichElementB];
if (chainParams.isSS == YES)
{
lnLikeA *= powerSS;
lnLikeB *= powerSS;
}
lnPriorA = curLnPr[whichElementA];
lnPriorB = curLnPr[whichElementB];
if (reweightingChars == YES)
{
if (chainParams.isSS == YES)
lnR = (tempB * (lnLikeStateAonDataB*powerSS + lnPriorA) + tempA * (lnLikeStateBonDataA*powerSS + lnPriorB)) - (tempA * (lnLikeA + lnPriorA) + tempB * (lnLikeB + lnPriorB));
else
lnR = (tempB * (lnLikeStateAonDataB + lnPriorA) + tempA * (lnLikeStateBonDataA + lnPriorB)) - (tempA * (lnLikeA + lnPriorA) + tempB * (lnLikeB + lnPriorB));
}
else
lnR = (tempB * (lnLikeA + lnPriorA) + tempA * (lnLikeB + lnPriorB)) - (tempA * (lnLikeA + lnPriorA) + tempB * (lnLikeB + lnPriorB));
if (lnR < -100.0)
r = 0.0;
else if (lnR > 0.0)
r = 1.0;
else
r = exp(lnR);
isSwapSuccessful = NO;
if (RandomNumber(seed) < r)
{
/* swap chain id's (heats) */
tempX = chainId[whichElementA];
chainId[whichElementA] = chainId[whichElementB];
chainId[whichElementB] = tempX;
if (reweightingChars == YES)
{
curLnL[whichElementA] = lnLikeStateAonDataB;
curLnL[whichElementB] = lnLikeStateBonDataA;
}
isSwapSuccessful = YES;
}
chI = chainId[whichElementA];
chJ = chainId[whichElementB];
if (chainId[whichElementB] < chainId[whichElementA])
{
chI = chainId[whichElementB];
chJ = chainId[whichElementA];
}
runId = chI / chainParams.numChains;
chI = chI % chainParams.numChains;
chJ = chJ % chainParams.numChains;
swapInfo[runId][chJ][chI]++;
if (isSwapSuccessful == YES)
swapInfo[runId][chI][chJ]++;
}
/* we need to communicate across processors */
else
{
if (reweightingChars == YES)
{
/* If we are reweighting characters, then we need to do an additional communication to
figure out the chainId's of the partner. We need to have this information so we can
properly calculate likelihoods with switched observations. */
if (areWeA == YES)
{
lnLikeStateAonDataB = 0.0;
myId = chainId[whichElementA];
ierror = MPI_Isend (&myId, 1, MPI_INT, procIdForB, 0, MPI_COMM_WORLD, &request[0]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
ierror = MPI_Irecv (&partnerId, 1, MPI_INT, procIdForB, 0, MPI_COMM_WORLD, &request[1]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
ierror = MPI_Waitall (2, request, status);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
for (d=0; d<numCurrentDivisions; d++)
{
m = &modelSettings[d];
tree = GetTree(m->brlens, whichElementA, state[whichElementA]);
lnL = 0.0;
m->Likelihood (tree->root->left, d, whichElementA, &lnL, partnerId);
lnLikeStateAonDataB = lnL;
}
}
else
{
lnLikeStateBonDataA = 0.0;
myId = chainId[whichElementB];
ierror = MPI_Isend (&myId, 1, MPI_INT, procIdForA, 0, MPI_COMM_WORLD, &request[0]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
ierror = MPI_Irecv (&partnerId, 1, MPI_INT, procIdForA, 0, MPI_COMM_WORLD, &request[1]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
ierror = MPI_Waitall (2, request, status);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
for (d=0; d<numCurrentDivisions; d++)
{
m = &modelSettings[d];
tree = GetTree(m->brlens, whichElementB, state[whichElementB]);
lnL = 0.0;
m->Likelihood (tree->root->left, d, whichElementB, &lnL, partnerId);
lnLikeStateBonDataA = lnL;
}
}
}
if (areWeA == YES)
{
/*curLnPr[whichElementA] = LogPrior(whichElementA);*/
/* we are processor A */
tempIdA = chainId[whichElementA];
lnLikeA = curLnL[whichElementA];
lnPriorA = curLnPr[whichElementA];
swapRan = RandomNumber(seed);
myStateInfo[0] = lnLikeA;
myStateInfo[1] = lnPriorA;
myStateInfo[2] = tempIdA;
myStateInfo[3] = swapRan;
myStateInfo[4] = 0.0;
if (reweightingChars == YES)
{
myStateInfo[2] = lnLikeStateAonDataB;
tempIdB = partnerId;
}
ierror = MPI_Isend (&myStateInfo, 5, MPI_DOUBLE, procIdForB, 0, MPI_COMM_WORLD, &request[0]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
ierror = MPI_Irecv (&partnerStateInfo, 5, MPI_DOUBLE, procIdForB, 0, MPI_COMM_WORLD, &request[1]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
ierror = MPI_Waitall (2, request, status);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
lnLikeA = curLnL[whichElementA];
lnLikeB = partnerStateInfo[0];
if (chainParams.isSS == YES)
{
lnLikeA *= powerSS;
lnLikeB *= powerSS;
}
lnPriorA = curLnPr[whichElementA];
lnPriorB = partnerStateInfo[1];
if (reweightingChars == YES)
lnLikeStateBonDataA = partnerStateInfo[2];
else
tempIdB = partnerStateInfo[2];
tempA = Temperature (tempIdA);
tempB = Temperature (tempIdB);
if (reweightingChars == YES)
{
if (chainParams.isSS == YES)
lnR = (tempB * (lnLikeStateAonDataB*powerSS + lnPriorA) + tempA * (lnLikeStateBonDataA*powerSS + lnPriorB)) - (tempA * (lnLikeA + lnPriorA) + tempB * (lnLikeB + lnPriorB));
else
lnR = (tempB * (lnLikeStateAonDataB + lnPriorA) + tempA * (lnLikeStateBonDataA + lnPriorB)) - (tempA * (lnLikeA + lnPriorA) + tempB * (lnLikeB + lnPriorB));
}
else
lnR = (tempB * (lnLikeA + lnPriorA) + tempA * (lnLikeB + lnPriorB)) - (tempA * (lnLikeA + lnPriorA) + tempB * (lnLikeB + lnPriorB));
if (lnR < -100.0)
r = 0.0;
else if (lnR > 0.0)
r = 1.0;
else
r = exp(lnR);
/* process A's random number is used to make the swap decision */
isSwapSuccessful = NO;
if (swapRan < r)
{
/* swap chain id's (heats) */
isSwapSuccessful = YES;
tempIdMy = chainId[whichElementA];
procIdPartner = procIdForB;
if (reweightingChars == YES)
chainId[whichElementA] = tempIdB;
else
chainId[whichElementA] = (int)(partnerStateInfo[2]);
if (reweightingChars == YES)
{
curLnL[whichElementA] = lnLikeStateAonDataB;
}
}
/* only processor A keeps track of the swap success/failure */
chI = tempIdA;
chJ = tempIdB;
if (tempIdB < tempIdA)
{
chI = tempIdB;
chJ = tempIdA;
}
runId = chI / chainParams.numChains;
chI = chI % chainParams.numChains;
chJ = chJ % chainParams.numChains;
swapInfo[runId][chJ][chI]++;
if (isSwapSuccessful == YES)
{
swapInfo[runId][chI][chJ]++;
/* exchange the move info */
for (i=0; i<numUsedMoves; i++)
{
myStateInfo[0] = usedMoves[i]->nAccepted[tempIdA];
myStateInfo[1] = usedMoves[i]->nTried[tempIdA];
myStateInfo[2] = usedMoves[i]->nBatches[tempIdA];
myStateInfo[3] = usedMoves[i]->nTotAccepted[tempIdA];
myStateInfo[4] = usedMoves[i]->nTotTried[tempIdA];
myStateInfo[5] = usedMoves[i]->lastAcceptanceRate[tempIdA];
if (usedMoves[i]->moveType->numTuningParams > 0)
myStateInfo[6] = usedMoves[i]->tuningParam[tempIdA][0];
else
myStateInfo[6] = 0.0;
ierror = MPI_Isend (&myStateInfo, 7, MPI_DOUBLE, procIdForB, 0, MPI_COMM_WORLD, &request[0]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
ierror = MPI_Irecv (&partnerStateInfo, 7, MPI_DOUBLE, procIdForB, 0, MPI_COMM_WORLD, &request[1]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
ierror = MPI_Waitall (2, request, status);
if (ierror != MPI_SUCCESS)
{
return (ERROR);
}
usedMoves[i]->nAccepted[tempIdB] = (int)partnerStateInfo[0];
usedMoves[i]->nTried[tempIdB] = (int)partnerStateInfo[1];
usedMoves[i]->nBatches[tempIdB] = (int)partnerStateInfo[2];
usedMoves[i]->nTotAccepted[tempIdB] = (int)partnerStateInfo[3];
usedMoves[i]->nTotTried[tempIdB] = (int)partnerStateInfo[4];
usedMoves[i]->lastAcceptanceRate[tempIdB] = partnerStateInfo[5];
if (usedMoves[i]->moveType->numTuningParams > 0)
usedMoves[i]->tuningParam[tempIdB][0] = partnerStateInfo[6];
usedMoves[i]->nAccepted[tempIdA] = 0;
usedMoves[i]->nTried[tempIdA] = 0;
usedMoves[i]->nBatches[tempIdA] = 0;
usedMoves[i]->lastAcceptanceRate[tempIdA] = 0.0;
usedMoves[i]->nTotAccepted[tempIdA] = 0;
usedMoves[i]->nTotTried[tempIdA] = 0;
if (usedMoves[i]->moveType->numTuningParams > 0)
usedMoves[i]->tuningParam[tempIdA][0] = 0.0;
}
}
}
else
{
/*curLnPr[whichElementB] = LogPrior(whichElementB);*/
/* we are processor B */
tempIdB = chainId[whichElementB];
lnLikeB = curLnL[whichElementB];
lnPriorB = curLnPr[whichElementB];
swapRan = -1.0;
myStateInfo[0] = lnLikeB;
myStateInfo[1] = lnPriorB;
myStateInfo[2] = tempIdB;
myStateInfo[3] = swapRan;
myStateInfo[4] = 0.0;
if (reweightingChars == YES)
{
myStateInfo[2] = lnLikeStateBonDataA;
tempIdA = partnerId;
}
ierror = MPI_Isend (&myStateInfo, 5, MPI_DOUBLE, procIdForA, 0, MPI_COMM_WORLD, &request[0]);
if (ierror != MPI_SUCCESS)
{
return (ERROR);